README.md

metadata

license: other
pretty_name: zinc_clean
tags:
  - chemistry
  - molecules
  - graph-generation
  - flow-matching
size_categories:
  - 100K<n<1M

nico8771/zinc_clean — cleaned ZINC-250k

Each row is a molecule as canonical SMILES plus RDKit-recomputed targets. Charged groups (N+/O-) are preserved.

Source: torch_molecule ZINC-250k (HuggingFace). Code: https://github.com/Nico-Conti/flow-matching-molecules (dataset/).

Schema

column	type	description
smiles	string	canonical, kekulizable, single-fragment SMILES (post-sanitize)
y	list[float]	RDKit targets, columns = logP, qed, SAS

Pipeline

1. Parse with RDKit; unparseable dropped.
2. Standardize — remove stereochemistry, sanitize (charges preserved; N+/O- kept).
3. Kekulize over atom vocab (C, N, O, F, P, S, Cl, Br, I, N+, O-); atoms outside the vocab dropped.
4. Round-trip check — smiles -> (X, E) -> mol -> smiles must reproduce the canonical molecule as a single fragment (filter applied).

Bonds use 4 classes (none / single / double / triple). Targets (logP, qed, SAS) are recomputed from the canonical SMILES with RDKit.

Drop / keep counts (this build)

outcome	count
drop_roundtrip	1
drop_vocab	2,005
kept	247,449

Kept: 247,449 molecules.